3) When you extract Cyko_03_31_14.7z, there will be a folder titled Cyko with the files. Next open HandbrakeCLI zip file and copy those files into the Cyko folder.

Cyko is basically a program with some presets installed on it which
makes it much easier to encode. The settings that I use are:
Target Quality: 23
Target Height: depends on the video
Target Audio: 48
The Preset that I choose is "slow" which is basically medium quality.
Tunes: for dramas, I use film.
As for Profiles, I never touch that.

It should look like this:

PS: I know that there is a newer/updated version, but I didn't like it much because it took too long to encode.